Nested Configuration Files Not Loaded in Claude Code Auto Mode

Since Claude Code v2.1.229, the enabled Auto Mode and Permission Bypass Mode add a 'Prioritize Bash Tool' instruction to sessions, causing an issue where nested CLAUDE.md files are not loaded. This instruction guides Claude to read and edit files using Bash commands such as cat and sed, but nested configuration files are only triggered when using the native Read tool, so the rules are ignored.

Severity of the Issue and Data Analysis

An analysis of one month of session logs (480 main sessions, 1,200 subagent sessions) by a developer revealed that in sessions with Bash-first mode enabled, 97% of file reads were performed via Bash, and the rate at which nested CLAUDE.md files were loaded before the first edit was only 10%. In contrast, the load rate was 79% in sessions where this mode was disabled.

• Rule Violations: The rule 'run terraform apply only on the main branch' in the infra/ folder was applied only 3 out of 30 times.
• Hooks Not Triggered: PostToolUse hooks that detect Edit or Write tools do not execute during Bash edits, causing 6 hooks, such as formatters and reminders, to be skipped in approximately 2/3 of edits.
• Impact on Subagents: In versions prior to v2.1.260, Subagents could not load nested CLAUDE.md files at all.

Solutions and Temporary Workarounds

Currently, Anthropic has not provided an official response or changelog update regarding related GitHub issues (such as #90450). The workarounds suggested by developers are as follows:

1. Root File Import: Import all nested files in the root CLAUDE.md using the @service/AGENTS.md format to ensure they are loaded at session start (increases token cost by approximately 3k).
2. Unofficial Environment Variable: Add "CLAUDE_CODE_THRIFTY_SONIC": "0" to settings.json to remove the Bash-first instruction while maintaining Auto Mode (confirmed in the v2.1.271 binary, may be removed in future versions).
3. Limitations of Path-Scoped Rules: Path-scoped rules in .claude/rules/ also rely solely on the Read tool and do not resolve this issue.